* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ratematrix’ ...
** this is package ‘ratematrix’ version ‘1.2.4’
** package ‘ratematrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-5) 14.3.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkq8CaT/R.INSTALL29da387d904f85/ratematrix/src'
g++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MultRegimeMCMC.cpp -o MultRegimeMCMC.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from MultRegimeMCMC.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
g++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ratematrix.so MultRegimeMCMC.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkq8CaT/R.INSTALL29da387d904f85/ratematrix/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkq8CaT/R.INSTALL29da387d904f85/ratematrix/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkq8CaT/R.INSTALL29da387d904f85/ratematrix/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ratematrix/00new/ratematrix/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘ratematrix’
    finding HTML links ... done
    anoles                                  html  
    centrarchidae                           html  
    checkConvergence                        html  
    computeESS                              html  
    continueMCMC                            html  
    estimateTimeMCMC                        html  
    extractCorrelation                      html  
    fastSimmap                              html  
    getStartPointFromPosterior              html  
    likelihoodFunction                      html  
    logAnalyzer                             html  
    makePrior                               html  
    mergePosterior                          html  
    mergeSimmap                             html  
    plotPrior                               html  
    plotRatematrix                          html  
    plotRootValue                           html  
    print.ratematrix_multi_chain            html  
    print.ratematrix_multi_mcmc             html  
    print.ratematrix_prior_function         html  
    print.ratematrix_prior_sample           html  
    print.ratematrix_single_chain           html  
    print.ratematrix_single_mcmc            html  
    ratematrix                              html  
    ratematrixJointMCMC                     html  
    ratematrixMCMC                          html  
    readMCMC                                html  
    readMCMC_Mk                             html  
    samplePrior                             html  
    simRatematrix                           html  
    testRatematrix                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ratematrix)